Zootopia In The Time Of Hydra
by tiagovelhoh
Summary: After a strange crash, both the SHIELD team and Gideon Malick find themselves in Zootopia! Nick, Judy, their friends, and the rest of Zootopia will find themselves in the middle of a struggle between SHIELD and HYDRA. What will Nick and Judy do when they are themselves thrown into the long war between the two sides that have been fighting since the dawn of HYDRA?
1. Chapter 1

**Hello everyone! Thank you for checking out my Crossover Story! If you have watched the show Agents of S.H.I.E.L.D, then this story may become confusing to you (SPOILER ALERT, THIS STORY TAKES PLACE AFTER THE MID SEASON FINALE OF SEASON 3). Also, if you have not checked out my other fan fiction (not a crossover) about Zootopia called "Their Savior", please check it out!**

 **PLEASE READ: In this story, it will be an alternate universe for AOS (Agents of S.H.I.E.L.D). In this story, as you will see this chapter, HIVE was successfully killed on the alien planet, but Ward survived.**

 **Hope you enjoy!**

The alien planet was a dark and desolate place. Everything was quiet and still on the entire planet, except for one place. The portal between this alien planet and earth stuck out of the ground in a swirling mess. A little ways away, the creature known as "Hive" lay face first in the sand. It had taken the body of Will, who had died trying to save Jemma from Hive. Behind Hive, Fitz tried to crawl away, only taking a moment to look behind him. Fitz saw Coulson and Ward fighting and punching. Ever since Grant Ward had betrayed Fitz and the rest of SHIELD, a strong hate grew in all of them against Ward, especially after Ward tried to kill them. When Fitz turned back to look at Hive, the monster was already getting back onto his feet and making his way to the portal. Fitz had to stop Hive from reaching the portal, or else Hive would dominate earth and possibly destroy it. Fitz leaped back onto his feet and ran for the gun that had been dropped in the sand. He picked it up and fired at Hive. The alien barely flinched as Fitz's shot hit him in the back. Fitz kept on shooting until finally Hive fell to the floor, but only for a moment.

Back on the Zephyr, Jemma, May, Bobby, Hunter, Joey, and Lincoln watched a map of the portal room.

"There! Look!" Jemma pointed to a large white dot on the screen. "The portal's open!"

"That's good!" Joey said.

"Yeah, but that's not." Hunter said, acknowledging all the little dots around the portal room. "Hydra's almost in!"

"All weapon systems go hot!" May ordered speaking to the rest of the crew on the Zephyr. "Stand by for my command."

On the wings of the Zephyr, parts of the wing retracted to show missiles ready to fire at the Hydra stronghold.

Back on the alien planet, Coulson and Ward continued to punch kick each other until Coulson got a good punch in and knocked Ward to the ground. Ward tried to get back up, but Coulson kicked him in the face.

"How many people?!" Coulson said angrily. "The lives you've taken!" Then Coulson punched Ward in the face, knocking the Hydra agent to the ground. "It's over Ward." Coulson said, looking down at the man who used to be a friend.

When Fitz saw Hive getting back up, he grabbed the backpack, dropped the gun, and pulled out a flare gun that was inside. Fitz walked over to Hive, aimed, and shot Hive in the back with a flare. Fitz watched as Hive's body caught on fire and burned.

Back in the portal room, Mack and Sky stood, pointing their guns at the portal. Sky looked at Mack and spoke "We're out of time" before collapsing from the pain and exhaustion of keeping the portal open.

On the alien planet, Fitz saw the portal begin to close, and shouted at Coulson who was still standing over Ward, "Coulson! The portal's closing!"

Coulson looked back down at Ward who lay there, groaning in pain. How badly Coulson wanted to kill Ward.

"It's finished!" Fitz yelled, "Leave him! We have to go!"

Coulson looked once again back down at Ward. Coulson thought about Rosalind, and how Ward had killed her in cold blood. Coulson fell to his knees, his hand moving to crush Ward's chest and kill him once in for all. Every bit of Coulson wanted to kill Ward, but Coulson knew it was not the right thing. Coulson, the director of SHIELD, grabbed Ward's shoulder and picked him up. As Coulson dragged Ward towards the portal, Fitz yelled. "What are you doing?! Leave him!"

Coulson ignored Fitz and continued to drag Ward to the Portal. "Help me with him!" He called to Fitz.

Fitz hated Ward with every inch of his soul. Ward had dropped him and Jemma into the ocean to die. Fitz wanted to leave Ward to a slow an painful death on Maveth (the planet). However, if he didn't help, Coulson would never make it in time. Coulson wasn't just Fitz's leader, he was a great friend to Fitz as well. Fitz and the rest of the team would be nothing without Coulson. So Fitz did his best to put aside his hate for Ward, and helped Coulson pick him up and carry him to the portal.

With the entire team safely on board the Zephyr, Ward in the medical bay, and the Hydra stronghold blown to pieces, the team was in the main living room. But instead of rejoicing, they were arguing. It seemed as the only person who didn't argue with Coulson bringing Ward back, was May. However, she didn't argue, not because she liked Ward, in fact she hated him too, May didn't argue because she knew that Coulson had done the right thing.

"How could you bring Ward back!" Jemma yelled angrily, "After everything he did to all of us!"

"You need to calm down agent Simmons!" May spoke before Coulson could say anything. "We all know that Hive can take the bodies of humans, if Coulson just killed Ward, Hive might have come back in Ward's body! Did you want that to happen?"

After this no one spoke for a while. They just stood and thought.

Finally Coulson spoke, "As soon as Ward is in good enough condition to leave med bay, we lock him up in the darkest and secret prison under SHIELD's control."

"Agreed." Sky spoke. Some of the others in the team nodded as well.

"Let's all get some rest." Coulson said.

Back at Gideon Malick's stonghold, Gideon was not in the best of moods. In the master bedroom, chairs and tables were being thrown around. Despite his older age, Gideon managed to smash some of his furniture into pieces. This was the result of all of his life's work being totally destroyed.

"SHIELD! They always come and ruin my work! I spent my whole life trying to bring him back, and so did my ancestors! But now... now the very being we devoted our lives to save... IS DEAD!" Gideon wailed and cursed. It was a strange sight, seeing the man who had so calmly taken control and never loose his head, finally enter a fit of absolute rage. To Gideon, his life no longer had any purpose.

Back on the SHIELD zephyr, the alarm began to sound. Filling the entire plan with flashing red light and loud noises.

"What's going on?!" Coulson asked, stepping into the flight room. "We only left the Hydra stronghold 20 minutes ago!"

"Director!" One of the pilots called to Coulson. "Something's wrong with the zephyr! It's starting to lose altitude!"

"Where are we?" May asked, also entering the flight room.

"We are currently flying over one of the more desolate parts of the Appalachian mountains! If we crash here, there will be no civilian casualties!" The co-pilot answered.

All of a sudden, an extremely loud BOOM was heard, and they all saw the wings begin to be violently torn off.

"Everyone get to the escape chamber!" Coulson ordered. "Now!" **(Sorry, I don't know what that flying box is called :P)**

Everyone ran for the flying white box that the team used for rescue operations and sometimes as a prison cell. As they ran, they all yelled to other agents to head to the chamber as well. Without the quinjet, the box would have to do. As they ran, the plane began to tilt forward, causing all sorts of objects to start to slide at them.

"Coulson!" May yelled, jumping over a table that hadn't been bolted down to the floor, and had been about to hit her. "What about Ward?!"

"Dammit!" Coulson cursed, only just remembering their prisoner. "I'll get him! The rest of you need to get to the chamber!"

"Coulson!" Hunter yelled, "We have probably less than 3 minutes before the plane crashes! Just leave Ward!"

But Coulson ignored Hunter and continued to run to the little med bay inside the zephyr. When Coulson reached the med bay, he found two nurses trying to pick up Ward.

"I got him!" Coulson yelled, picking up Ward. "Just go to the med bay!". As Coulson dragged him down the hall, Coulson said to Ward,"I don't even know why I'm rising so much just to save you.", even though he knew Ward was too drugged to understand him.

When Coulson finally squeezed Ward and himself into the chamber, Bobby yelled,

"Ok! That's everyone! Close this thing and eject us!"

Lincoln put in the security code on the screen on the side of the wall before closing the door and pressing the button that should have ejected them from Zephyr One. But it didn't work. Lincoln tried two more times before cursing,

"Crap!" He yelled, "It won't work!"

"10 seconds!" The pilot yelled. He had been keeping his eye on a machine that told them how close they were to the ground.

"Everyone hold on!" May yelled.

And then everything was consumed by a bright red light.

Back at Gideon Malick's home, one of his agent was struggling to gather the courage to knock on Gideon's door. He had heard the sounds of Gideon breaking things, and Gideon was a bad person to make angry. The raging thunderstorm outside did not help either. Finally the Hydra agent took in a deep breath and knocked.

"Enter" came Gideon's reply a few moments later. When the Hydra agent entered, he saw the destruction of Gideon's room. It seemed as every bit of furniture was in pieces, even the ones made out of stone. On the walls there were spots of blood were Gideon had punched the wall until his knuckles bled.

"Sir." The Hydra agent began, "We've just received word that a SHIELD plane just crashed nearby one of our outposts in the Appalachians. We believe it may be the same one that destroyed our stronghold recently."

As soon as he finished talking, Gideon was on his feet and standing before the agent, a look of absolute hatred in his eyes.

"Assemble everyone! If even one of those SHIELD rats are alive, I want them to suffer! I will be going there myself!"

"Y- yes sir!" The Hydra agent stuttered, before saying the infamous phrase.

"Heil Hydra!"

12 Hydra helicopters hovered above the wreckage. Gideon gazed upon the wreckage with total satisfaction.

"By the look of this wreckage, they all suffered a horrible death. A pity I couldn't deal with them myself. But it does not matter, they are dead now." Gideon chuckled to himself.

Suddenly Gideon's celebration was cut short by a strange red mist seeping out of the ground.

"What the hell is that?!" One Hydra agent yelled.

"I don't like this," Gideon spoke to his pilot, "Get us out of here."

But before they could leave, the mist sprang into the air and began to surround the helicopters.

"Get us out of here!" Gideon yelled, suddenly afraid. "Now!"

But it was too late.

The entire SHIELD team stood before the white chamber. They were on a grassy hill, under a beautiful sky. Everything about this scenario was crazy. For one, they were all alive and well, then there was the fact that they were standing on a small grassy hill in a peaceful and bright day. They had crashed into the mountains during a stormy night. But the craziest part? Before them stood a magnificent city unlike they had ever seen. A few miles to their left, a bullet train passed by and it heading towards the city.

"Where are we?" Joey asked.

 **Hey guys! That's all for chapter one! Again, thank you all for reading my story! Please check out my other story! I will see all you guys... next chapter!**


	2. Welcome to Zootopia

**Hey guys! I am finally back with another chapter of this crossover story! If you follow my other story then you will know that I have been very busy recently. I have one announcement for today!**

 **Announcement 1: Thank you to Lavakey, Readerfever, anthonyluetmer1, bsmith1138, viny231, wnaruto616, A Little Lost 1, Darman Skirata, Omegashark18, Rjdle, and trebor1212 for supporting my story!**

The SHIELD team stood together in awe and confusion.

"Where are we?" Joey asked.

"I don't know." Coulson answered, "Fitz Simmons?"

"Well, sir, without our proper lab equipment, or any equipment for that matter, there isn't much Fitz and I can do." Jemma spoke.

"Then what do you suggest?" May asked.

"Well, considering we have nothing, all we can do is go to the city and ask around." Fitz replied before Jemma could speak.

"That's like a 10 mile walk to that city, and nothing along the way." Hunter pointed out.

"Then we better get walking" Said Coulson.

"Wait!" Bobby called out, "What about Ward?"

"I told you Coulson," Said Ward, stepping forward with a gun in his hand. "We're all part of something bigger. I don't know what my role is yet, but I'll find out eventually."

The all the SHIELD agents who had pistols on them pulled them out and pointed them at Ward.

"Ward!" Bobby yelled, "Put the gun down!"

Ward dropped the gun and put his hands up.

"Woah, woah, woah." He spoke, "Let's all calm down here, the gun wasn't even loaded."

"Where did he even get that gun?" Daisy asked.

"Uhh, I think he took mine." The pilot told Daisy.

"You two," Coulson pointed at two of the other agents, "Secure Ward, I want to get to the city before nightfall."

"Yes sir!"Came the reply.

Inside of the city, in a small apartment building, a grey bunny dressed in a police uniform stood impatiently in front of one of the doors.

"Nick! I know you're in there! If you don't get your tail out here right now, we're going to be late for work again!" The bunny yelled.

Suddenly the door swung open to reveal a red fox in a police uniform.

"Relax Carrots!" Nick said with a smile, "I'm ready to go!"

Judy huffed.

"Plus," Nick continued, handing his partner a coffee cup, "I made you some coffee!"

"You're lucky I like coffee so much." Judy spoke, taking the cup from Nick.

When the two of them made it two Precinct One, Judy was in a much better mood than before. It was usually hard for her to stay in a sour mood for much longer than 15 minutes.

"Good morning Clawhauser!" Judy called to the donut loving cheetah.

"Morning you two!" Clawhauser replied, "You better head into the bullpen, it starts in five minutes!"

"See you later buddy!" Nick said before entering the bullpen with Judy.

10 Minutes Later

All the officers in the bullpen were whispering to each other. Chief Bogo had not shown up yet.

"He's five minutes late!" Judy quietly exclaimed to Nick.

Nick was the only relaxed one in the room, he had his feet on the table and was checking his phone.

"Don't worry." Nick brushed it off. "The Chief is a busy mammal, he's probably just caught up in something important."

Judy relaxed a little, "Yeah," She agreed, "You're probably right."

15 Minutes Later

"Ok," Nick said, "Now I'm worried. He's 20 minutes late!" No longer did Nick have his phone out, or laying his feet on the table.

"Me too." Judy agreed.

"Should some mammal go up and check if he didn't die in that ominously dark office of his?" Nick asked.

Fortunately that was not the case as Chief Bogo finally stepped into the Bullpen.

As the Chief walked over to his podium, Judy whispered to Nick.

"Something's not right."

Nick nodded, she was right. Bogo had a look on his face that looked to be some sort of mix of confusion, angst, and worry; and to add to all that, he didn't even have his glasses or his paperwork.

Everyone in the bullpen was silent, waiting for the chief to finally speak. When he did however, his voice had a tone that they had never heard from him before. Fear.

"Approximately 25 minutes ago, the Zootopian Department of Defense spotted 12 unidentified helicopters flying towards the city."

If it was even possible, the room became even quieter.

Chief Bogo continued, "I have a transcript of what was spoken when the department of defense made contact through radio with one of the helicopters."

No body spoke as Chief Bogo cleared his throat and read the transcript.

" _Dep. of Defense agent: "This is the Zootopia Department of Defense, you are approaching the city from the northern side without any sort of registration or identification of yourself or the other helicopters with you. Please identify yourself."_

 _Unknown: "You will find out soon enough."_

 _Dep. of Defense agent: "Who are you?"_

 _Unknown: "Salvation"_ "

No mammal in the bullpen had expected this. Before any mammal could ask any questions, Bogo continued talking.

"The mammal on the other end sounds like a nut job, but considering he does have 8 attack helicopters and 4 transport helicopters, we must treat this as an eminent threat to our city."

"What are we going to do Chief?" Judy asked.

"I have been informed that these helicopters are about 10 minutes from reaching the city, so we will all be ready in our cars to secure the area that they plan to land in." The Chief answered. "Now go!"

8 Minutes Later

"I can see them in the horizon!" Judy informed the rest of her comrades through the radio.

Sure enough, 12 helicopters flying in a "v" formation were flying straight towards them. They were getting closer by the second.

"I have never seen any sort of helicopter like that before." Nick spoke to his partner.

"Me neither." Judy agreed.

When the helicopters were almost right above them, Judy started the car, and began to follow them.

Nick grabbed the radio, "Officer Hopps and I are currently following them! They seem to be heading towards central park!"

"All officers converge on that position!" Nick and Judy heard Bogo order over the radio.

Judy sped towards the park, it was hard because all around them citizens were stopping and looking up. When they were almost at the park, they ere joined by 10 heavy SWAT trucks.

In Bogo's police cruiser, he pulled out his cell phone and called one of his contacts.

"Those rooftop SAMs better be up and running in case I need them!" He bellowed.

A voice on the other end responded, "The Surface to Air Missiles are ready at your disposal. Should I fire?"

"No." Bogo answered, "I don't want to have to make this any worse than it already is. We're in the heart of the city, to many citizens could get hurt."

All the police and SWAT vehicles mad a perimeter around the park as the 12 helicopters began to land.

"McHorn! Francine!" Bogo ordered into the radio, "You two come with me! The rest of you guys stay back, but be prepared! Use lethal force if necessary!"

The buffalo, rhino, and elephant approached the helicopters. When the helicopters landed however, they were not prepared for what they saw.

The four transport helicopters opened their doors and a swarm of soldiers lined up in formation in front of the lead helicopter, which happened to be the biggest.

Judy and Nick were watching from a distance. "What are they?" Judy asked, completely confused as to the appearance of these creatures. They ere unlike anything she had ever seen before.

"You ask me as if I know, Carrots." Nick replied, equally dumbfounded.

"Uh, Sir?" Officer Francine asked Chief Bogo. "I have never seen this species in my life. What are they?"

For once, Bogo was extremely confused as well.

"I have no clue." The Chief replied.

Then the lead helicopter opened up, and out stepped a man with the air of a leader. Bogo could tell that this creature, whatever it was, was in charge of the rest; even if it did look a lot older than the rest.

As the thing approached, Bogo yelled for him to stop. "If you take one more step!" The cap buffalo warned, "Your helicopters will be destroyed and you will be shot!"

The creature stopped walking, but gave the chief an amused look.

"What are you?" Bogo asked.

The creature laughed as if it were all a joke to him. "Why I'm a human!" He responded.

No mammal knew what a human was, but Bogo decided he would find out more about that later.

"Who are you, and what business do you have here?" Bogo asked.

The human spoke with a sense of pride and power, "My name is Gideon Malick! And I am the director of SHIELD!"

 **Hey guys! I hope you liked this chapter! Sorry it took so damn long to be finished! I have been hanging out with my Brazilian family so much! I have been having so much fun here. I love Brazil. Anyways, I'll see you guys next time!**


	3. It's Coming Back!

**Hey guys, I know it has been ages since I updated this series, but I promise you, I have not forgotten it. I will be starting it back up soon. If you have any ideas for this, just PM me or leave a comment.**


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